Davida Suzanne Smyth

Davida Suzanne Smyth
Texas A&M University – San Antonio · Department of Biology

PhD
Wastewater Epidemiology, AMR in the Built Environ, Science Ed as Civic Ed, looking for collaborators and funders!

About

111
Publications
10,484
Reads
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2,279
Citations
Introduction
Additional affiliations
August 2018 - August 2021
New School
Position
  • Professor (Associate)
September 2021 - present
Texas A&M University-San Antonio
Position
  • Associate Professor of Microbiology
July 2016 - July 2018
Mercy University
Position
  • Chair

Publications

Publications (111)
Article
Full-text available
Background Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains, or species to infer the relative abundances of sequences present in a sample. This observation plays an important role in the analysis of diverse microbial communities, where targeted sequencing of 16S and 18S rRNA, both well-known hypervaria...
Article
Full-text available
Peer-Led Team Learning (PLTL) is a pedagogical approach that has been shown to benefit all students, especially underrepresented minority students and peer leaders in Science, Technology, Engineering, and Mathematics (STEM) disciplines. In this work, we present results from our study of the impact of PLTL on our peer leaders from a controlled imple...
Preprint
Full-text available
Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains or species to infer the relative abundances of sequences present in a sample. This observation plays an important role in the analysis of diverse microbial communities, where targeted sequencing of 16S and 18S rRNA, both well-known hypervariable genomic...
Article
Full-text available
At the onset of the 2019 coronavirus disease (COVID-19) pandemic, it was clear that we needed to support public education on the science of vaccines. This project was born of that need and led to the development of comprehensive educational materials that addressed the process of science, severe acute respiratory syndrome coronavirus 2 biology, vac...
Article
Staphylococcus haemolyticus is a normal inhabitant of healthy skin and is also an emerging cause of nosocomial infections in the immunocompromised. S. haemolyticus infections often lead to bacteremia, septicemia, peritonitis, endocarditis and various other outcomes. The goal of this project was to establish an invertebrate infection model for study...
Article
Full-text available
SARS-CoV-2 surveillance of viral populations in wastewater samples is recognized as a useful tool for monitoring epidemic waves and boosting health preparedness. Next generation sequencing of viral RNA isolated from wastewater is a convenient and cost-effective strategy to understand the molecular epidemiology of SARS-CoV-2 and provide insights on...
Article
Full-text available
ABSTRACT ePortfolios are digital repositories where students can curate papers, projects, and reflections from individual or multiple courses across the disciplines and in a variety of formats to showcase their learning. This transparent and portable medium, which enables students to document their knowledge and abilities for assessment and career...
Article
Full-text available
The transmission of airborne pathogens is considered to be the main route through which a number of known and emerging respiratory diseases infect their hosts. While physical distancing and mask wearing may help mitigate short-range transmission, the extent of long-range transmission in closed spaces where a pathogen remains suspended in the air re...
Preprint
Full-text available
New York City's ongoing wastewater monitoring program tracked trends in sewershed-level SARS-CoV-2 loads starting in the fall of 2020, just before the start of the City's second wave of the COVID-19 outbreak. During a five-month study period, from November 8, 2020 to April 11, 2021, viral loads in influent wastewater from each of New York City's 14...
Article
Full-text available
Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we deep sequence most of the receptor binding domain coding sequence of the S protein o...
Article
Full-text available
SARS-CoV-2 viral loads in New York City were significantly correlated with clinical case rates in corresponding sewersheds.
Article
Full-text available
The following protocol describes our workflow for processing wastewater with the goal of detecting the genetic signal of SARS-CoV-2. The steps include pasteurization, virus concentration, RNA extraction, and quantification by RT-qPCR. We include auxiliary steps that provide new users with tools and strategies that will help troubleshoot key steps i...
Preprint
Full-text available
The following protocol describes our workflow for processing wastewater with the goal of detecting the genetic signal of SARS-CoV-2. The steps include pasteurization, virus concentration, RNA extraction, and quantification by RT-qPCR. We include auxiliary steps that provide new users with tools and strategies that will help troubleshoot key steps i...
Preprint
Full-text available
Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we amplified regions of the SARS-CoV-2 Spike protein gene from RNA acquired from all 14...
Preprint
The following protocol describes our workflow for processing wastewater with the goal of detecting the genetic signal of SARS-CoV-2. The steps include pasteurization, virus concentration, RNA extraction, and quantification by RT-qPCR. We include auxiliary steps that provide new users with tools and strategies that will help troubleshoot key steps i...
Preprint
Full-text available
The transmission of airborne pathogens via aerosols is considered to be the main route through which a number of known and emerging respiratory diseases infect their hosts. It is therefore essential to quantify airborne transmission in closed spaces and determine what recommendations should be implemented to minimize the exposure to the pathogen in...
Preprint
Full-text available
Monitoring SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To date, most data on SARS-CoV-2 genetic diversity has come from the sequencing of clinical samples, but such studies may suffer limitations due to cost...
Preprint
Full-text available
The following protocol describes our workflow for processing wastewater with the goal of detecting the genetic signal of SARS-CoV-2. The steps include pasteurization, virus concentration, RNA extraction, and quantification by RT-qPCR. We include auxiliary steps that provide new users with tools and strategies that will help troubleshoot key steps i...
Article
Full-text available
Effectively analyzing literature can be challenging for those unfamiliar with studies from rapidly evolving research fields. Previous studies have shown that incorporating primary literature promotes scientific literacy and critical thinking skills. We’ve used collaborative note-taking and annotation of peer-reviewed articles to increase student en...
Preprint
Full-text available
The following protocol describes our workflow for processing wastewater with the goal of detecting the genetic signal of SARS-CoV-2. The steps include pasteurization, virus concentration, RNA extraction, and quantification by RT-qPCR. We include auxiliary steps that provide new users with tools and strategies that will help troubleshoot key steps i...
Article
Full-text available
Undergraduate research (UR) is a high-impact practice (HIP) to engage undergraduate student in science, technology, engineering and mathematics (STEM), especially from underrepresented groups. UR experiences (UREs) can be integrated into the classroom, making authentic research experiences inclusive and available to all students. However, developin...
Article
Full-text available
Honey has a stable physiochemical composition that contributes to its long shelf life and has been noted as an antimicrobial substance for centuries. Although it is common knowledge that honey affords some antimicrobial properties, the specific mechanisms behind this remain elusive. This paper hypothesizes that the microorganisms in certain raw hon...
Article
Full-text available
Acinetobacter baumannii is an extremely versatile multidrug resistant pathogen with a very high mortality rate therefore, it has become crucial to understand the host response during its infection. Given the importance of mice for modelling infection and their role in pre-clinical drug development equal emphasis should be placed on the utilization...
Chapter
In this chapter, we will introduce the concepts of growth, competition, and adaptation using bacteria. We will use both simulation and laboratory-based exercises and provide practice with critical skills to assess your understanding throughout the chapter. The chapter ends by focusing on the capacious and global problem of antibiotic resistance, co...
Poster
Full-text available
Peer-Led Team Learning (PLTL) is a teaching method where teams of peer leaders lead small group workshops designed to reinforce content covered in course lecture. This method was first used in chemistry courses and has been shown to be particularly beneficial for minority students in STEM (Gosser Jr. & Roth, 1998; Gosser Jr., et al, 2001). In addit...
Conference Paper
While teaching microbiology at undergraduate institutions, it has often crossed my mind how similar our college ecosystems are to microbial ecosystems. It is possible to identify the layers and the structures that stratify the institution and to elucidate the various interactions that are manifest among the persons residing in these educational hab...
Article
Full-text available
Maintaining undergraduate interest in STEM is a formidable challenge. Numerous studies have reported that structured, authentic research experiences in the classroom increase retention rates and introduce students to the skills needed to conduct independent research as upperclassmen and beyond. Most importantly, these strategies are inclusive, enab...
Article
Full-text available
We have designed and implemented a novel microbiology elective course "Microbiology of Urban Spaces" to provide students with a transformative education in microbial ecology and genomics. It champions the values of general education while making sure students are well equipped for their future careers. Infusing my personal research into the course...
Article
Full-text available
This paper describes the structure and activities of READ (Reading Effectively Across the Disciplines), a pilot initiative to improve students’ critical reading skills, disciplinary literacy and academic success. READ employs a multimodal design that consists of faculty training in disciplinary literacy instruction and curricular enhancement, devel...
Article
The SaPIs are a cohesive subfamily of extremely common phage-inducible chromosomal islands (PICIs) that reside quiescently at specific att sites in the staphylococcal chromosome and are induced by helper phages to excise and replicate. They are usually packaged in small capsids composed of phage virion proteins, giving rise to very high transfer fr...
Article
Full-text available
The current study identified bacterial factors that may improve management of methicillin-resistant Staphylococcus aureus (MRSA) nosocomial pneumonia. Isolates were obtained from 386 patients enrolled in a randomized, controlled study of antibiotic efficacy. Isolates were screened for production of virulence factors and for vancomycin susceptibilit...
Article
Full-text available
A total of 434 methicillin-resistant Staphylococcus aureus (MRSA) baseline isolates were collected from subjects enrolled in a prospective, double-blind randomized trial comparing linezolid versus vancomycin for the treatment of nosocomial pneumonia. Isolates were susceptibility tested by broth microdilution, examined for inducible clindamycin resi...
Article
Full-text available
Inactivating mutations in the Staphylococcus aureus virulence regulator agr are associated with worse outcomes in bacteremic patients. However, whether agr dysfunction is primarily a cause or a consequence of early bacteremia is unknown. Analysis of 158 paired S. aureus clones from blood and nasal carriage sites in individual patients revealed that...
Conference Paper
Full-text available
Background / Purpose: A total of 435 methicillin-resistant Staphylococcus aureus (MRSA) baseline isolates were collected from subjects enrolled in a linezolid phase IV nosocomial pneumonia (NP) clinical trial. The aim of this study was to characterize this collection of MRSA strains. Main conclusion: Each region had two predominant clones resp...
Article
Full-text available
Staphylococcus aureus infections are a significant cause of morbidity and mortality in health care settings. S. aureus clinical isolates vary in the function of the accessory gene regulator (agr), which governs the expression of virulence determinants, including surface and exoproteins, while agr activity has been correlated with patient outcome an...
Article
Full-text available
Staphylococcal chromosomal cassette mec (SCCmec) is a mobile genetic element that carries resistance genes for beta-lactam antibiotics. Coagulase-negative staphylococci, such as S. epidermidis, are thought to be a reservoir of diverse SCCmec elements that can spread to the most virulent staphylococcal species, S. aureus, but very little is known ab...
Article
Full-text available
Phenotypic biotyping has traditionally been used to differentiate bacteria occupying distinct ecological niches such as host species. For example, the capacity of Staphylococcus aureus from sheep to coagulate ruminant plasma, reported over 60 years ago, led to the description of small ruminant and bovine S. aureus ecovars. The great majority of sma...
Article
Full-text available
Phenotypic biotyping has traditionally been used to differentiate bacteria occupying distinct ecological niches such as host species. For example, the capacity of Staphylococcus aureus from sheep to coagulate ruminant plasma, reported over 60 years ago, led to the description of small ruminant and bovine S. aureus ecovars. The great majority of sma...
Article
Introduction Overview of The Staphylococcal Population Structure Staphylococcal Population Structure in Specific Disease Contexts Origin and Maintenance of Staphylococcal Genetic Variation Macroevolutionary Considerations and Concluding Remarks References Appendix 1—Diversity and Differentiation
Data
SCCmec type III variants as detected by the multiplex PCR assay. (A) Map shows relative locations of select loci, not to scale. (B) Table lists presence or absence of multiplex PCR products using primers from reference 45. ccrC was also amplified, independently, using primers from reference 49. Patterns for types III–IIIB are described in reference...
Data
Characteristics of study isolates. (0.08 MB XLS)
Data
Characteristics of the discovery panel of isolates. PFGE was done with standard methods. Table lists strain name, geographic source and date of isolation, haplotype defined from 32 loci, SCCmec multiplex PCR type and ccrB:dru sequence type. (0.43 MB TIF)
Article
Full-text available
The methicillin-resistant Staphylococcus aureus (MRSA) clonal group known as ST239-MRSA-III is notable for its hybrid origin and for causing sustained hospital epidemics worldwide since the late 1970s. We studied the population structure of this MRSA clonal group using a sample of 111 isolates that were collected over 34 years from 29 countries. Ge...
Article
Full-text available
Since the year 2000, linezolid has been used in the United States to treat infections caused by antimicrobial-resistant Gram-positive cocci. At present, linezolid-resistant (Linr) Staphylococcus aureus and Staphylococcus epidermidis strains are rare and the diversity of their genetic backgrounds is unknown. We performed sequence-based strain typing...
Article
Full-text available
A novel composite transposon (Tn6072) resembling staphylococcal cassette chromosome mercury (SCCHg) was identified in a collection of sequence type (ST) 239 methicillin (meticillin)-resistant Staphylococcus aureus (MRSA) isolates from Romanian hospitals. Tn6072 is homologous to the 5′ region of SCCHg found in staphylococcal cassette chromosome mec...
Article
Full-text available
Staphylococcus aureus is an important pathogen of man, but is also able to colonize and cause disease in a wide variety of mammals and birds. An extended multilocus sequencing approach, involving multilocus sequence typing (MLST), sas typing, spa typing and agr typing, was used to examine the molecular diversity of 118 S. aureus isolates recovered...
Article
At a time when the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) was changing, we sought to characterize several genotypic markers and glycopeptide susceptibility features of clinical isolates from patients with bacteraemia. One hundred and sixty-eight MRSA bloodstream isolates obtained from three multicentre clinical...
Article
Full-text available
Twenty genes encoding enterotoxin and enterotoxin-like proteins have been described in Staphylococcus aureus strains. Five of these occur commonly in the enterotoxin gene cluster (egc: selo, selm, sei, seln and seg). In the sei-seln intergenic region, two pseudogenes, psient1 and psient2, can be present or an additional gene designated selu or a va...